Installation

Prerequisites

Python 3.10 or newer
uv (recommended) — used throughout this project for dependency and environment management

Installing the server

The server is published on PyPI as rnacentral-mcp-server. The simplest option is to let uvx fetch and run it on demand — no explicit install step required:

uvx --from rnacentral-mcp-server run-server

To install it into an environment instead:

pip install rnacentral-mcp-server
# or
uv add rnacentral-mcp-server

Either way, the console script run-server becomes available.

From source

For development, clone the repository and sync dependencies:

git clone https://github.com/rnacentral/rnacentral-mcp-server.git
cd rnacentral-mcp-server
uv sync

This creates a .venv/ and installs the server plus its runtime dependencies. The console script run-server becomes available inside that environment.

Connecting the server to your LLM

The server speaks the Model Context Protocol over stdio, so any MCP-capable client can launch it. The examples below cover the most common clients — if you’re using something different, point it at the same uvx ... run-server command.

The commands below use the PyPI package. To run the latest unreleased code instead, replace rnacentral-mcp-server with git+https://github.com/rnacentral/rnacentral-mcp-server.git.

Claude Desktop

Add the server to claude_desktop_config.json (on macOS: ~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "rnacentral": {
      "command": "uvx",
      "args": [
        "--from",
        "rnacentral-mcp-server",
        "run-server",
        "--log-dir",
        "/Users/YOUR_USERNAME/logs/rnacentral"
      ]
    }
  }
}

--log-dir is optional; pass it if you want on-disk logs for debugging.

Restart Claude Desktop and the rnacentral tools should appear in the tool picker.

Claude Code

Register the server with claude mcp add:

claude mcp add rnacentral -- uvx --from rnacentral-mcp-server run-server

Other MCP clients

Any client that launches an MCP server over stdio works. The command to run is:

uvx --from rnacentral-mcp-server run-server

Or, from a local clone:

uv run run-server --log-dir ./logs

Development mode

Run the server under the MCP Inspector to try tools interactively:

uv run mcp dev rnacentral_sequence_search/server.py

Building these docs locally

uv sync --extra docs
uv run sphinx-build -b html docs docs/_build/html

Or, from inside docs/, make html.